diff --git a/build.sh b/build.sh index 19039f7..4edda9d 100755 --- a/build.sh +++ b/build.sh @@ -1,5 +1,5 @@ #!/bin/bash -e - +python fix_jupyterlite_html.py content cd tskit-launcher/ jlpm install jlpm run build diff --git a/content-hash.txt b/content-hash.txt index af71b3c..b7401f3 100644 --- a/content-hash.txt +++ b/content-hash.txt @@ -1 +1 @@ -05cfda449cc14ff90cee5a0e1f904008f159ce3fd094eb319c55c4fce01076f6 +b93af6127eb04d9bf604e2432d529f1ea6b25ee943b25da5137b91426f6c00b0 diff --git a/content/tskit.ipynb b/content/tskit.ipynb index 3a89440..12b7625 100644 --- a/content/tskit.ipynb +++ b/content/tskit.ipynb @@ -28,343 +28,7 @@ "outputs": [ { "data": { - "text/html": [ - "\n", - "
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Populations1224 Bytes\n", - " ✅\n", - "
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08 July, 2025 at 10:31:57 AMmsprime1.3.4sim_mutations\n", - "
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version: 1.3.4
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\n", - "
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rate: 0.1
model: None
start_time: None
end_time: None
discrete_genome: None
keep: None
random_seed: 741366272
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node: treebeard
release: 5.15.0-133-generic
version: #144-Ubuntu SMP Fri Feb 7
20:47:38 UTC 2025
machine: x86_64
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08 July, 2025 at 10:31:47 AMmsprime1.3.4sim_ancestry\n", - "
\n", - " Details\n", - " \n", - "
\n", - " \n", - "
\n", - " dict\n", - " schema_version: 1.0.0
\n", - "
\n", - " software:\n", - "
\n", - " dict\n", - " name: msprime
version: 1.3.4
\n", - "
\n", - "
\n", - "
\n", - "
\n", - " parameters:\n", - "
\n", - " dict\n", - " command: sim_ancestry
samples: 100
demography: None
sequence_length: 1000
discrete_genome: None
recombination_rate: 0.1
gene_conversion_rate: None
gene_conversion_tract_length: None
population_size: None
ploidy: None
model: None
initial_state: None
start_time: None
end_time: None
record_migrations: None
record_full_arg: None
additional_nodes: None
coalescing_segments_only: None
num_labels: None
random_seed: 1166325161
replicate_index: 0
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node: treebeard
release: 5.15.0-133-generic
version: #144-Ubuntu SMP Fri Feb 7
20:47:38 UTC 2025
machine: x86_64
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\n \n Tree Sequence \n
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Nodes1 76548.3 KiB\n \n
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Provenance TimestampSoftware NameVersionCommandFull record
08 July, 2025 at 10:31:57 AMmsprime1.3.4sim_mutations\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: msprime
version: 1.3.4
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: sim_mutations
\n
\n tree_sequence:\n
\n dict\n __constant__: __current_ts__
\n
\n
\n
rate: 0.1
model: None
start_time: None
end_time: None
discrete_genome: None
keep: None
random_seed: 741366272
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: treebeard
release: 5.15.0-133-generic
version: #144-Ubuntu SMP Fri Feb 7
20:47:38 UTC 2025
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.11.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
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\n
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\n dict\n version: 0.6.4
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08 July, 2025 at 10:31:47 AMmsprime1.3.4sim_ancestry\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: msprime
version: 1.3.4
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: sim_ancestry
samples: 100
demography: None
sequence_length: 1000
discrete_genome: None
recombination_rate: 0.1
gene_conversion_rate: None
gene_conversion_tract_length: None
population_size: None
ploidy: None
model: None
initial_state: None
start_time: None
end_time: None
record_migrations: None
record_full_arg: None
additional_nodes: None
coalescing_segments_only: None
num_labels: None
random_seed: 1166325161
replicate_index: 0
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: treebeard
release: 5.15.0-133-generic
version: #144-Ubuntu SMP Fri Feb 7
20:47:38 UTC 2025
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.11.11
\n
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\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
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\n tskit:\n
\n dict\n version: 0.6.4
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\n gsl:\n
\n dict\n version: 2.6
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\n ", "text/plain": [ "" ] @@ -408,4 +72,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} +} \ No newline at end of file diff --git a/fix_jupyterlite_html.py b/fix_jupyterlite_html.py new file mode 100644 index 0000000..ef1b0b5 --- /dev/null +++ b/fix_jupyterlite_html.py @@ -0,0 +1,211 @@ +#!/usr/bin/env python3 +""" +Fix JupyterLite HTML comma issue by consolidating multi-line HTML outputs to single lines. + +This script processes .ipynb files and fixes the issue where JupyterLite adds commas +to the beginning of each line in HTML output. It does this by converting multi-line +HTML strings in cell outputs to single-line strings. + +Usage: + python fix_jupyterlite_html.py [notebook_file_or_directory] + +If no argument is provided, it will process all .ipynb files in the current directory. +""" + +import json +import os +import sys +import argparse +from pathlib import Path +from typing import List, Dict, Any + + +def fix_html_output(output: Dict[str, Any]) -> bool: + """ + Fix HTML output by consolidating multi-line strings to single lines. + + Args: + output: A notebook cell output dictionary + + Returns: + bool: True if the output was modified, False otherwise + """ + modified = False + + # Check if this is an HTML output + if output.get("output_type") == "execute_result" or output.get("output_type") == "display_data": + data = output.get("data", {}) + + # Fix text/html output + if "text/html" in data: + html_content = data["text/html"] + + # If it's a list of strings (multi-line), join them + if isinstance(html_content, list): + # Join all lines into a single string + single_line_html = "".join(html_content) + data["text/html"] = single_line_html + modified = True + print(f" Fixed HTML output: converted {len(html_content)} lines to single line") + + # If it's a single string with newlines, we could optionally process it too + # but the main issue is with the list format + + return modified + + +def fix_notebook(notebook_path: Path) -> bool: + """ + Fix a single notebook file. + + Args: + notebook_path: Path to the notebook file + + Returns: + bool: True if the notebook was modified, False otherwise + """ + print(f"Processing: {notebook_path}") + + try: + # Read the notebook + with open(notebook_path, 'r', encoding='utf-8') as f: + notebook = json.load(f) + + modified = False + + # Process each cell + for cell_idx, cell in enumerate(notebook.get("cells", [])): + # Check cell outputs + for output_idx, output in enumerate(cell.get("outputs", [])): + if fix_html_output(output): + modified = True + + # Write back if modified + if modified: + with open(notebook_path, 'w', encoding='utf-8') as f: + json.dump(notebook, f, indent=1, ensure_ascii=False) + print(f" ✓ Fixed and saved: {notebook_path}") + return True + else: + print(f" No changes needed: {notebook_path}") + return False + + except Exception as e: + print(f" ✗ Error processing {notebook_path}: {e}") + return False + + +def find_notebooks(path: Path) -> List[Path]: + """ + Find all .ipynb files in a directory or return the single file. + + Args: + path: Path to search (file or directory) + + Returns: + List of notebook file paths + """ + if path.is_file(): + if path.suffix == '.ipynb': + return [path] + else: + print(f"Warning: {path} is not a .ipynb file") + return [] + + elif path.is_dir(): + notebooks = list(path.rglob('*.ipynb')) + # Filter out checkpoint files + notebooks = [nb for nb in notebooks if '.ipynb_checkpoints' not in str(nb)] + return notebooks + + else: + print(f"Error: {path} does not exist") + return [] + + +def main(): + parser = argparse.ArgumentParser( + description="Fix JupyterLite HTML comma issue in notebook files", + formatter_class=argparse.RawDescriptionHelpFormatter, + epilog=""" +Examples: + python fix_jupyterlite_html.py # Fix all .ipynb files in current directory + python fix_jupyterlite_html.py notebook.ipynb # Fix a specific notebook + python fix_jupyterlite_html.py content/ # Fix all notebooks in content/ directory + python fix_jupyterlite_html.py --dry-run # Show what would be changed without modifying files + """ + ) + + parser.add_argument( + 'path', + nargs='?', + default='.', + help='Path to notebook file or directory (default: current directory)' + ) + + parser.add_argument( + '--dry-run', + action='store_true', + help='Show what would be changed without modifying files' + ) + + args = parser.parse_args() + + # Convert to Path object + search_path = Path(args.path) + + # Find all notebooks + notebooks = find_notebooks(search_path) + + if not notebooks: + print("No notebook files found.") + return 1 + + print(f"Found {len(notebooks)} notebook(s) to process:") + for nb in notebooks: + print(f" - {nb}") + print() + + if args.dry_run: + print("DRY RUN MODE - No files will be modified") + print() + + # Process each notebook + total_modified = 0 + for notebook_path in notebooks: + if not args.dry_run: + if fix_notebook(notebook_path): + total_modified += 1 + else: + # For dry run, just check if it would be modified + try: + with open(notebook_path, 'r', encoding='utf-8') as f: + notebook = json.load(f) + + would_modify = False + for cell in notebook.get("cells", []): + for output in cell.get("outputs", []): + if output.get("output_type") in ["execute_result", "display_data"]: + data = output.get("data", {}) + if "text/html" in data and isinstance(data["text/html"], list): + would_modify = True + break + if would_modify: + break + + if would_modify: + print(f" Would fix: {notebook_path}") + total_modified += 1 + else: + print(f" No changes needed: {notebook_path}") + + except Exception as e: + print(f" Error checking {notebook_path}: {e}") + + print(f"\nSummary: {total_modified} notebook(s) {'would be' if args.dry_run else 'were'} modified") + + return 0 + + +if __name__ == "__main__": + sys.exit(main())